All submarines are a pain in the backside- part of the appeal. ::)
A few pointers. Most successful seehunds run with a dive module- a cylinder of between 100-120mm diameter and about 500mm long. The ballast tank is part of this cylinder, and either a piston tank (best IMO, but not cheap unless you DIY) or a water pump is used for controlling the ballast volume. The latter consists of either a geared pump or a centrifugal windscreen washer type pump, pumping into a sealed tank. The tank fills to about 70% as the air compresses above the water, so you need to oversize the tank by 30% to allow for this.
A pinch valve stops the compressed air blowing the water back out though the pump. This system is reliable and inexpensive and works well. If you use a peristaltic pump, then you can dispense with a pinch valve, as they self seal. The snag with this type of pump is that they are very slooooow, and they also need to be run either way. Norbert uses a perstaltic pump on the Delta. In the case of that boat the ballast volume isn't too great (about 250ml), so the system works well enough- all the same builders of this boat have commented that the tank(bag) takes a while to fill.
The snag with using a bag and compressed air, is that the air in the bag is compressible. This means as you dive deeper, the bag will constrict and your boat will get heavier and sink (out of control). There are two ways around this-
1. Trim your boat so it is just positively buoyant with bag fully deflated i.e. nothing further to compress. Then dive dynamically.
2. Put the bag inside a cylinder which has a kingston valve at the bottom. This will prevent water pressure from acting on the bag.
The first way is simpler.
Andy